Graph Complexity Analysis tools
$ GCAtools.sh -h
GCAtools
Usage: GCAtools -f <clusterfolder> [options]
Description:
Core workflow of GCAtools
Options:
-h Show this message and exit
-f <dir> Folder of cluster files
-t <str> Type of cluster files (dna or pep) [default dna]
-d <dir> Output file in <dir> [default ./GCAout]
-s Set super5 module for muscle [default False]
-n <int> Number of threads [default 36]
Author: Yumin Huang; ymhuang@fafu.edu.cn
$ GCAtools_prepare.sh -h
Tool: GCAtools prepare
Usage: GCAtools_prepare -g <gff3 file> -f <genome file> [options]
Description:
Prepare gene clusters for input
Options:
-h Show this message and exit
-g <string> gff3 file
-f <string> genome fasta file
-c <string> cds fasta file [default False]
-p <string> pep fasta file [default False]
-d <string> output dir [default ./results]
-o <string> output prefix [default out]
-m <int> minimal cluster size [default 2]
Author: Yumin Huang; ymhuang@fafu.edu.cn